deploy: c2f8928

FAIR-Chem · Jul 14, 2024 · 5df42db · 5df42db
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diff --git a/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt b/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt
diff --git a/_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt b/_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt
@@ -1,16 +1,16 @@
-2024-07-13 04:31:12 (INFO): Running in non-distributed local mode
-2024-07-13 04:31:12 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
-2024-07-13 04:31:13 (INFO): amp: true
+2024-07-14 21:59:31 (INFO): Running in non-distributed local mode
+2024-07-14 21:59:31 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-07-14 21:59:32 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-07-13-04-30-56
-  commit: aacb883
+  checkpoint_dir: ./checkpoints/2024-07-14-22-00-32
+  commit: c2f8928
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-07-13-04-30-56
+  logs_dir: ./logs/tensorboard/2024-07-14-22-00-32
   print_every: 10
-  results_dir: ./results/2024-07-13-04-30-56
+  results_dir: ./results/2024-07-14-22-00-32
   seed: 0
-  timestamp_id: 2024-07-13-04-30-56
-  version: 0.1.dev1+gaacb883
+  timestamp_id: 2024-07-14-22-00-32
+  version: 0.1.dev1+gc2f8928
 dataset: {}
 evaluation_metrics:
   metrics:
@@ -113,20 +113,20 @@ test_dataset:
 trainer: ocp
 val_dataset: {}
 
-2024-07-13 04:31:13 (INFO): rank: 0: Sampler created...
-2024-07-13 04:31:13 (INFO): Batch balancing is disabled for single GPU training.
-2024-07-13 04:31:13 (INFO): Loading model: gemnet_t
-2024-07-13 04:31:15 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-07-13 04:31:15 (WARNING): log_summary for Tensorboard not supported
-2024-07-13 04:31:16 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-07-13 04:31:16 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. 
-2024-07-13 04:31:16 (WARNING): Scale factor comment not found in model
-2024-07-13 04:31:16 (INFO): Predicting on test.
+2024-07-14 21:59:32 (INFO): rank: 0: Sampler created...
+2024-07-14 21:59:32 (INFO): Batch balancing is disabled for single GPU training.
+2024-07-14 21:59:32 (INFO): Loading model: gemnet_t
+2024-07-14 21:59:34 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-07-14 21:59:34 (WARNING): log_summary for Tensorboard not supported
+2024-07-14 21:59:34 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-07-14 21:59:34 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. 
+2024-07-14 21:59:34 (WARNING): Scale factor comment not found in model
+2024-07-14 21:59:34 (INFO): Predicting on test.
 device 0:   0%|                                           | 0/3 [00:00<?, ?it/s]/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
-device 0:  33%|███████████▋                       | 1/3 [00:05<00:11,  5.70s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:08<00:03,  3.96s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:11<00:00,  3.49s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:11<00:00,  3.80s/it]
-2024-07-13 04:31:27 (INFO): Writing results to ./results/2024-07-13-04-30-56/ocp_predictions.npz
-2024-07-13 04:31:27 (INFO): Total time taken: 11.534403562545776
-Elapsed time = 17.8 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:03<00:06,  3.13s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:03,  3.02s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:08<00:00,  2.97s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.01s/it]
+2024-07-14 21:59:43 (INFO): Writing results to ./results/2024-07-14-22-00-32/ocp_predictions.npz
+2024-07-14 21:59:43 (INFO): Total time taken: 9.158892154693604
+Elapsed time = 15.3 seconds

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diff --git a/_images/c84cdf1f1c563ab775269291ed00d65161ab7c669704177bfc44d6c7082ee750.png b/_images/c84cdf1f1c563ab775269291ed00d65161ab7c669704177bfc44d6c7082ee750.png
diff --git a/_images/d5aa0b1d568bc4551e72d7676f8149ff52662ef2090741232c280992d0c18083.png b/_images/d5aa0b1d568bc4551e72d7676f8149ff52662ef2090741232c280992d0c18083.png
diff --git a/_images/db683f9834a520f8261218b0cc097a56141eade11e7b9604c0754b69e071993f.png b/_images/db683f9834a520f8261218b0cc097a56141eade11e7b9604c0754b69e071993f.png
diff --git a/_images/fe7270b7e99d723bc5a122a1a7a8706382e0c57ef0e9dca9f82ce88125d25b98.png b/_images/fe7270b7e99d723bc5a122a1a7a8706382e0c57ef0e9dca9f82ce88125d25b98.png
diff --git a/_sources/index.md b/_sources/index.md
@@ -8,7 +8,10 @@
 <h4 align="center">
 
 ![tests](https://github.com/FAIR-Chem/fairchem/actions/workflows/test.yml/badge.svg?branch=main)
-[![Static Badge](https://img.shields.io/badge/python-3.9%2B-blue)](https://www.python.org/downloads/)
+![documentation](https://github.com/FAIR-Chem/fairchem/actions/workflows/deploy_docs.yml/badge.svg?branch=main)
+![Static Badge](https://img.shields.io/badge/python-3.9%2B-blue)
+
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/FAIR-Chem/fairchem?quickstart=1)
 
 </h4>
 

diff --git a/core/fine-tuning/fine-tuning-oxides.html b/core/fine-tuning/fine-tuning-oxides.html
@@ -828,7 +828,7 @@ <h1>Fine tuning a model<a class="headerlink" href="#fine-tuning-a-model" title="
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time 67.8 seconds.
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time 67.4 seconds.
 </pre></div>
 </div>
 <img alt="../../_images/e09235df67f6a4f604e2dc396140b3979de3a415db6696093790df3189ca2edf.png" src="../../_images/e09235df67f6a4f604e2dc396140b3979de3a415db6696093790df3189ca2edf.png" />
@@ -907,7 +907,7 @@ <h1>Fine tuning the checkpoint<a class="headerlink" href="#fine-tuning-the-check
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2339/1448814737.py:12: DeprecationWarning: Please use atoms.calc = calc
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2280/1448814737.py:12: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 </pre></div>
 </div>
@@ -1200,7 +1200,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 <span class="expanded">Hide code cell output</span>
 </summary>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time = 205.9 seconds
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time = 203.2 seconds
 </pre></div>
 </div>
 </div>
@@ -1216,7 +1216,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&#39;fine-tuning/checkpoints/2024-07-13-04-26-40-ft-oxides&#39;
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&#39;fine-tuning/checkpoints/2024-07-14-21-54-08-ft-oxides&#39;
 </pre></div>
 </div>
 </div>
@@ -1275,7 +1275,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/d5aa0b1d568bc4551e72d7676f8149ff52662ef2090741232c280992d0c18083.png" src="../../_images/d5aa0b1d568bc4551e72d7676f8149ff52662ef2090741232c280992d0c18083.png" />
+<img alt="../../_images/2afa38ee2ad4f3a3071f9f940aa53f830cf5c83ce9bf222f0930cf66f6b1622f.png" src="../../_images/2afa38ee2ad4f3a3071f9f940aa53f830cf5c83ce9bf222f0930cf66f6b1622f.png" />
 </div>
 </div>
 <div class="cell docutils container">
@@ -1286,7 +1286,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>New MAE = 0.042 eV/atom
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>New MAE = 0.789 eV/atom
 </pre></div>
 </div>
 </div>
@@ -1305,7 +1305,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/c84cdf1f1c563ab775269291ed00d65161ab7c669704177bfc44d6c7082ee750.png" src="../../_images/c84cdf1f1c563ab775269291ed00d65161ab7c669704177bfc44d6c7082ee750.png" />
+<img alt="../../_images/4824685f0ad98d72e49a4607601630c480c1bb562b7de0372abf12f6a4814109.png" src="../../_images/4824685f0ad98d72e49a4607601630c480c1bb562b7de0372abf12f6a4814109.png" />
 </div>
 </div>
 <p>It is possible to continue refining the fit. The simple things to do are to use more epochs of training. Eventually the MAE will stabilize, and then it may be necessary to adjust other optimization parameters like the learning rate (usually you decrease it).</p>

diff --git a/core/gotchas.html b/core/gotchas.html
@@ -923,7 +923,7 @@ <h1>I get wildly different energies from the different models<a class="headerlin
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 </pre></div>
 </div>
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2609/1677958285.py:11: DeprecationWarning: Please use atoms.calc = calc
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2621/1677958285.py:11: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 </pre></div>
 </div>
@@ -960,7 +960,7 @@ <h1>I get wildly different energies from the different models<a class="headerlin
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 </pre></div>
 </div>
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2609/2284884232.py:9: DeprecationWarning: Please use atoms.calc = calc
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2621/2284884232.py:9: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 </pre></div>
 </div>
@@ -989,11 +989,11 @@ <h1>I get wildly different energies from the different models<a class="headerlin
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 </pre></div>
 </div>
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2609/898007276.py:7: DeprecationWarning: Please use atoms.calc = calc
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2621/898007276.py:7: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.6891541481018066
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.680762767791748
 </pre></div>
 </div>
 </div>
@@ -1458,7 +1458,7 @@ <h1>To tag or not?<a class="headerlink" href="#to-tag-or-not" title="Link to thi
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2609/3906293788.py:3: DeprecationWarning: Please use atoms.calc = calc
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2621/3906293788.py:3: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 </pre></div>
 </div>
@@ -1502,11 +1502,11 @@ <h1>To tag or not?<a class="headerlink" href="#to-tag-or-not" title="Link to thi
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2609/4094489779.py:3: DeprecationWarning: Please use atoms.calc = calc
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2621/4094489779.py:3: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>-0.42973634600639343
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>-0.4297374486923218
 </pre></div>
 </div>
 </div>
@@ -1553,21 +1553,21 @@ <h1>Stochastic simulation results<a class="headerlink" href="#stochastic-simulat
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 </pre></div>
 </div>
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2609/3095522216.py:11: DeprecationWarning: Please use atoms.calc = calc
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2621/3095522216.py:11: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 </pre></div>
 </div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.2139868021011353 1.655421765979762e-06
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+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.2139868259429931 1.5295996601434173e-06
+1.213986873626709
+1.2139837741851807
+1.2139875888824463
 1.2139866352081299
-1.2139835357666016
 1.213986873626709
-1.2139892578125
+1.213984489440918
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-1.2139861583709717
-1.2139887809753418
-1.2139880657196045
-1.2139854431152344
+1.213986873626709
+1.2139883041381836
+1.213989019393921
 </pre></div>
 </div>
 </div>
@@ -1605,11 +1605,11 @@ <h1>The forces don’t sum to zero<a class="headerlink" href="#the-forces-don-t-
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 </pre></div>
 </div>
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2609/2981184886.py:11: DeprecationWarning: Please use atoms.calc = calc
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2621/2981184886.py:11: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 </pre></div>
 </div>
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 </pre></div>
 </div>
 </div>
@@ -1622,7 +1622,7 @@ <h1>The forces don’t sum to zero<a class="headerlink" href="#the-forces-don-t-
 </div>
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 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([-5.6461431e-08, -7.6834112e-09, -1.1920929e-07], dtype=float32)
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([-6.0361344e-08, -2.6542693e-08,  7.1525574e-07], dtype=float32)
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